How should I understand this sentence?

Question

How should I understand the following sentence?

Missing until recently were fossils clearly intermediate, or transitional, between land mammals and cetaceans.

This from the excerpt of an article:

It should be obvious that cetaceans---whales, porpoises, and dolphins---are mammals. They breathe through lungs, not through gills, and give birth to live young. Their streamlined bodies, the absence of hind legs, and the presence of a fluke and blowhole cannot disguise their affinities with land-dwelling mammals. However, unlike the cases of sea otters and pinnipeds (seals, sea lions, and walruses, whose limbs are functional both on land and at sea), it is not easy to envision what the first whales looked like. Extinct but already fully marine cetaceans are known from the fossil record. How was the gap between a walking mammal and a swimming whale bridged? Missing until recently were fossils clearly intermediate, or transitional, between land mammals and cetaceans.

Added:

Is "clearly intermediate, or transitional, between land mammals and cetaceans" a clause? It seems that something is omitted here.

Answer 1

Missing until recently were fossils [clearly] [intermediate,] [or transitional,] [between land mammals and cetaceans].

In your sentence, the adjective intermediate modifies fossils. This adjective is again modified by the adverb clearly. The adjective transitional is in apposition to intermediate and so also modifies it, or it could be said to be parallel to it: in that case, both adjectives modify fossils directly and should be in bold. Thirdly, intermediate is modified by the prepositional phrase between land mammals and cetaceans.

The following is my paraphrase of the sentence. Until recently, certain fossils were missing. What kind of fossils? Fossils that are clearly intermediate, or transitional, between land mammals and cetaceans.

There are various reasons why adjectives may sometimes come after the noun they modify; see this question for some thoughts about the subject: the superlative + noun + possible.

Answer 2

Fossils ... were missing until recently.

In other words, for a long time nobody had them, but now they do.

"clearly intermediate" modifies "Fossils". "or transitional" is an alternative to the word "intermediate". "between ... cetaceans" is a prepositional phrase used to modify "fossils"... same as saying "the rabbit on the log".

Answer 3

fossils [that were] clearly intermediate, or transitional, between land mammals and cetaceans were missing until recently.

In other words, there was a gap or a lacking in the fossil record between land mammals and cetaceans. Recent discoveries have filled that gap.